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* gn/packages/python.scm (python-h5py-2): New variable.
* gn/packages/machine-learning.scm (tensorflow-native): Remove comments.
* gn/packages/ratspub.scm (use-corrected-inputs): New procedure.
(genecup-with-tensorflow-native, genecup-latest-with-tensorflow-native):
Use use-corrected-inputs.
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curl-minimal has been removed from upstream Guix.
* gn/packages/bioinformatics.scm (vg)[inputs]: Use curl instead of
curl-minimal.
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* gn/packages/python.scm (python-rdflib-shim)[source]: Add snippet to
use any version of python-rdflib-jsonld.
[propagated-inputs]: Replace python-rdflib-jsonld-0.6.1 with
python-rdflib-jsonld.
(python-rdflib-jsonld-0.6.1): Remove variable.
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* gn/packages/bioinformatics.scm (bh20-seq-resource-for-service): New
variable.
* gn/services/bh20-seq-resource-container.scm
(covid19-pubseq-configuration): Use it by default.
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* gn/packages/bioinformatics.scm (bh20-seq-resource)[arguments]: Add
phase to hardcode path to minimap2.
[inputs]: Add minimap2.
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* gn/packages/bioinformatics.scm (bh20-seq-resource): Update to
1.0-4.2ae7191.
[source]: Adjust snippet for changes in source.
[arguments]: Skip tests.
[propagated-inputs]: Add python-shexc-0.7. Remove python-dateutil,
python-flask, python-pycurl, python38-ruaml.yaml-0.15.76, clustalw,
python-twint.
[native-inputs]: Remove git, python-oauth2client, python-uritemplate.
Replace python-pytest-4 with python-pytest-5, python-pytest-runner-2
with python-pytest-runner-4.
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* gn/packages/python.scm (python-pytest-runner-4): New variable.
* gn/packages/bioinformatics.scm (python-pytest-runner-2): MOve to
python.scm
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* gn/packages/python.scm (python-pyshex): Downgrade to 0.7.14.
[arguments]: Disable tests. Add phase to fix compatibility with
rdflib-6. Adjust custom 'check phase.
[propagated-inputs]: Remove python-chardet. Replace python-pyshexc with
python-pyshexc-0.7, python-rdflib-shim with python-rdflib,
python-sparqlsluper with python-sparql-slurper.
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* gn/packages/python.scm (python-py-dateutil): New variable.
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* gn/packages/python.scm (python-pyshexc-0.7): New variable.
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* gn/packages/python.scm (python-pytest-5): New variable.
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* gn/packages/python.scm (python-arvados-python-client): Update to 2.5.0.
[source]: Add snippet to not limit the maximum version of pycurl.
[propagated-inputs]: Add python-google-api-core-1, python-google-auth-1,
python-protobuf, python-pyparsing-2.4.7, python-ruamel.yaml. Remove
python38-ruaml.yaml-0.15.76, python-setuptools, python-oauth2client,
python-uritemplate.
(python38-ruaml.yaml-0.15.76): Remove variable.
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* gn/packages/python.scm (python-shexjsg): Update to 0.8.2.
[arguments]: Remove custom 'patch-source phase. Update custom 'check
phase.
[propagated-inputs]: Remove python-antlr4-python3-runtime,
python-certifi, python-chardet, python-idna, python-isodate,
python-requests, python-urllib3.
[native-inputs]: Add python-rdflib-shim, python-requests. Remove
python-pyparsing, python-pyshexc, python-rdflib, python-rdflib-jsonld,
python-six, custom test-suite git checkout.
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* gn/packages/python.scm (python-sparqlslurper): New variable.
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* gn/packages/python.scm (python-rdflib-shim): New variable.
(python-rdflib-jsonld-0.6.1): New variable.
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* gn/packages/python.scm (python-pyshex): Update to 0.8.1.
[arguments]: Remove custom 'patch-source phase. Update custom 'check
phase.
[propagated-inputs]: Add python-chardet, python-rdflib-shim,
python-sparqlslurper. Remove python-rdflib, python-rdflib-jsonld,
python-pbr, python-sparql-slurper.
[native-inputs]: Add python-pbr, python-unitttest2.
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* gn/packages/python.scm (python-pyshexc): Update to 0.9.1.
[arguments]: Update custom 'check phase.
[propagated-inputs]: Add python-chardet, python-rdflib-shim,
python-shexjsg. Remove python-rdflib, python-rdflib-jsonld,
python-requests.
[native-inputs]: Add python-pbr, python-requests. Remove python-shexjsg,
custom test-suite git checkout.
(python-shexjsg-min): Remove variable.
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* gn/packages/python.scm (python-pyjsg): Update to 0.11.10.
[arguments]: Remove 'patch-source phase. Skip 1 set of tests in custom
'check phase.
[propagated-inputs]: Move python-requests ...
[native-inputs]: ... to here. Add python-unittest2. Remove test-suite
checkout.
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* gn/packages/python.scm (python-antlr4-python3-runtime): Update to
4.9.3.
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* gn/packages/python.scm (python-pytest-4)[native-inputs]: Add
python-atomicwrites.
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As part of improving the security of passwords, this commit adds
python-argon-cffi that enables use of the better Argon2 password
hashing algorithm, rather than the dated bcrypt that is a tad
vulnerable to offline cracking.
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* gn/packages/genenetwork.scm: (python-email-validator): New
dependency
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* gn/packages/gemini.scm: Import (gnu packages compression) and (guix
download).
(tissue): Update to 0.1.0.
[source]: Use url-fetch.
[native-inputs]: Add lzip.
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* gn/packages/gemini.scm (guile-xapian-latest): New variable.
(tissue): Use guile-xapian-latest.
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* gn/packages/genenetwork.scm: (python-authlib): New dependency
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Flask session already handles a lot of the house-keeping involved with
server-side sessions: this commit adds it as a dependency to avoid
having to do the house-keeping manually.
* gn/packages/genenetwork.scm: (python-flask-session): New dependency
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* gn/packages/genenetwork.scm (genenetwork3): Add python-authlib as a
dependency to genenetwork3
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* gn/packages/python-web.scm: (python-authlib): New package.
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This reverts commit fb631515ccf985e6e89c6cb03a86833aa3b963c6.
rust-quick-csv-0.1 isn't actually in Guix yet.
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* gn/packages/crates-io.scm (rust-clap-4): Change from
rust-terminal-size-0.2 which is undefined to rust-terminal-size-0.1
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* gn/packages/julia.scm (julia-visuals): slurp in sexps to fix the
package definition.
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* gn/packages/crates-io.scm (rust-quick-csv-0.1): Remove package that
is also defined in mainline guix
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* gn/packages/genenetwork.scm (genenetwork3): Update to version
0.1.0-2.e781996
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